Claude Code, Skill
Bench To Paper Skills
Agent skills for computational biology that stop instead of guessing — a public accession to a pipeline sample sheet, a run manifest to a methods paragraph — and a playbook for using them without letting the agent fill in what it was not told.
Compatibility: Not stated.
Grade B
Minor issues only, no Medium or High. Worth a quick look at the findings below before installing.
Not a guarantee. A hygiene check of the source at the commit shown, not a security audit.
NETWORK_NO_FIXED_HOST SECRETS_PATH_UNCONFIRMED
Why this grade
- NETWORK_NO_FIXED_HOST Low
Makes a network call whose host is not written as a fixed address.
skills/accession-to-samplesheet/scripts/samplesheet.py, line 140
def fetch(accession: str, *, save_raw: Path | None = None) -> tuple[list[dict], Source] | Refusal: - SECRETS_PATH_UNCONFIRMED Low
The Secrets check reports a credential or environment file, but no quoted line shows a recognisable path.
.gitignore, line 8
# or anything already tracked - that needs the secret scan + pre-commit hook (spec §8.5).
Any High, or two or more Medium findings, give D. One Medium gives C. Low findings or a security Note give B. Each code names a finding behind the letter.
Grades are a hygiene check of the source at the commit shown, on the date checked, not a security audit or a guarantee. The free directory grades are automated. Before release, a PlugVet engineer reviews every paid report and any grade we hold back, including all F grades, against the source code and the evidence we quote.
What was checked
Plain notes from the hygiene checks.
Permissions
Pass
No shell or command execution found, and no extra permission was declared.
Install and update
Pass
No install-time script found, and dependencies are pinned or absent.
Network
Concern
can reach a host that is not written as a fixed address.
NETWORK_NO_FIXED_HOST
skills/accession-to-samplesheet/scripts/samplesheet.py, line 140
def fetch(accession: str, *, save_raw: Path | None = None) -> tuple[list[dict], Source] | Refusal:
skills/accession-to-samplesheet/scripts/samplesheet.py, line 145
with urllib.request.urlopen(request, timeout=60) as response:
skills/accession-to-samplesheet/scripts/samplesheet.py, line 438
fetched = fetch(accession, save_raw=args.save_raw)
Secrets
Concern
reads a credential or environment file.
SECRETS_PATH_UNCONFIRMED
.gitignore, line 8
# or anything already tracked - that needs the secret scan + pre-commit hook (spec §8.5).
Agent instructions
Pass
No instruction to ignore earlier instructions or to hide a step.
Obfuscation
Pass
No encoded or minified payload found.
Licence
Pass
A licence file is present (LICENSE).
Maintainer activity
Pass
The latest commit is within the last 365 days.
Note
Hygiene check of commit c16db896f67b. can reach a host that is not written as a fixed address. reads a credential or environment file.
Date and source
Date checked:
github.com
Commit graded: c16db896f67b2f11f67d12f145fd4f04b2e09b1a
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